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include proteins of same type from different species. For example, photosynthetic reaction centers from and are considered unique. Structures of mutagenized versions of proteins already in the database are excluded as unique. Proteins that differ only by substrate bound or by physiological state are also excluded. Structures 'obsoleted' by the PDB are not included.

Total number of PDB coördinate files, including those for unique proteins. This number reflects the fact that published reports of structures often include several coördinate files describing, for example, the protein in different crystal forms, or with different bound substrates.

Pre-Publication Structures

A word about the new interface to the protein table.

Links to the Protein Data Bank Site

Links to the Structural Biology Knowledgebase Site

The table above is initially presented in a collapsed form, and the user can expand different sections of the table, or the entire table, and bookmark different sections of the table, or a fully expanded table version of the page, using the , , , and icons on the left margin of the table section headers.

The table provides useful information about integral membrane proteins whose crystallographic, or sometimes NMR or cryo-EM, structures have been determined to a resolution sufficient to identify TM helices of helix-bundle membrane proteins (typically 4 - 4.5Å). Reference is made to all of the protein types whose structures have been determined. We have attempted to make the database as inclusive as possible. If you find errors or omissions, please send a message to
Stephen White
.

Bombyx
mori
(Dazao strain) larvae were reared on fresh mulberry leaves in a dedicated silkworm rearing room at ambient temperature (23–27 °C). Genomic DNA samples were separately isolated from virgin female and male individuals with tissue DNA kits (OMEGA, Norcross, GA). In the case of W contigs that had autosomal or Z paralogs, primers for genomic DNA PCR were designed considering the differences between the autosomal or Z paralogs and the W sequence at the 3’ end of the primer. PCR was performed with GO Taq DNA Polymerase (Promega, Madison, WI;
Supplementary Table S1–S3
), RNA was isolated from individual embryos following the traditional Trizol method (Ambion, Carlsbad, CA) using the total RNA isolation protocol according to the manufacturer’s instructions. Residual DNA in samples was used to identify the gender of each embryo with the W_seq1 marker (
Supplementary Table S1
). Total RNA (following DNase treatment) was subjected to reverse transcription using a PrimeScript
TM
RT Master Mix (Perfect Real Time; TaKaRa, Kusatsu, Japan) in 50 μl reaction volume (2500 ng total RNA) and then diluted 5-fold. One μg of cDNA was used in 10 μl PCR reaction volume. Small RNAs (following DNase treatment) were subjected to reverse transcription using a Mir-X™ miRNA First-Strand Synthesis Kit (TaKaRa, Kusatsu, Japan). qPCR was performed with SYBR Premix Ex (TaKaRa, Kusatsu, Japan).

Although most of the
B. mori
W chromosome is composed of TEs whose copies are widely distributed on autosomes or on the Z chromosome, still some subtle variations such as single nucleotide polymorphisms (SNPs) can be observed only on W chromosome. Such W-specific variations may produce W-specific short sequences called
k
-mers.

For obtaining these possible W-specific
k
-mers, we tried to find an optimum
k
value (sequence length).
K
= 15, which is a typical value used for filtering errors in short reads,
11
,
19
is suitable for female-specific (W-specific)
k
-mers in
B. mori
. We counted the frequencies of each 15-mer separately in female and male sequence data and created a parameter called KQ. For a given
k
-mer
K
i, KQ(
k
i) =
M
(
k
i)/
F
(
k
i), where
M
(
k
i) is the frequency of
K
i in male reads and
F
(
k
i) denotes the frequency of
K
i in female reads. As females and males share the same complement of autosomes, autosomal 15-mers are present in both female and male sequencing data in roughly the same quantities. Therefore, autosomal 15-mers have KQ values distributed around one (
Fig.1
). As males have two Z chromosomes while females have only one, the Z-specific 15-mers have KQ values distributed around two. Since unique W chromosomal 15-mers are present only in female sequencing data, these KQ values localize to zero. We also applied KQ to
D. melanogaster
and
An. gambiae
[
Fig.1
, exchange
M
(
k
i) and
F
(
k
i) position in XX/XY species]. The results were similar to
B. mori
, which confirms that KQ may be applied to most sexually heterogametic species.